... if everything is going plug in based...
and in the jar is a part of the past.
Is it now theoretically possible to make a plug in that would tweek BTW to make it forge compatable?
I've not looked too heavily into the 1.6.1 release, yet, but from my understanding, the conflict between jarmods like BetterThanWolves and Forge has more to do with several mods trying to rewrite the same Java MineCraft-vanilla-basic class (and sometimes method) in contradictory ways. Moving to binary patches won't really change that, as long as the underlying conflict remains. It might be theoretically possible to overwrite both the Forge /and/ BTW versions into some cross-compatible result. I'm not sure it'd be any easier than modifying the class files is today, though, and doing so without violating copyright may not be possible.
((And that's ignoring the politics of the situation.))
I don't see anything in 1.6.1 that BetterThanWolves will have particular difficulty adjusting to, outside of the time investment in compatibility with resource packs / new MCP names.
So, how exactly are jar mods dead?
It remains possible, but manually doing so (or using programs like MultiMC to do so) should be far less necessary, including for Forge itself, due to the system automatically creating things. CPW says that the next version of Forge will be acting from a binary patch method, instead of manually inserted files with duplicated source code.